{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T02:08:02Z","timestamp":1790647682919,"version":"4.1.0"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":28,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We respond to concerns regarding fundamental data quality issues in datasets used for machine learning prediction of enzyme optimal pH (pHopt). We re-examined six questioned protein entries by tracing their annotated pH values to the original literature. Our analysis confirmed substantial discrepancies for several entries, including incorrect experimental values, misassigned protein identities, and proteins lacking the reported catalytic activity, whereas one entry was consistent with the literature. These findings support the need for rigorous verification of biochemical data underlying predictive models. We emphasize that careful literature based curation is essential for improving dataset reliability and model validity, and future iterations of pHopt predictors will be developed using more rigorously validated datasets.<\/jats:p>","DOI":"10.1093\/bib\/bbag537","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T01:54:30Z","timestamp":1790646870000},"source":"Crossref","is-referenced-by-count":0,"title":["Response to \u201cCaution: Fundamental data quality issues underlying intelligent prediction of enzyme optimal pH\u201d"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1936-1223","authenticated-orcid":false,"given":"Sizhe","family":"Qiu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology , Meilong Road 130, Xuhui district, Shanghai 200237 ,","place":["China"]},{"name":"Department of Engineering Science, University of Oxford , Parks Road, Oxford OX1 3PJ ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5974-247X","authenticated-orcid":false,"given":"Aidong","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Engineering Science, University of Oxford , Parks Road, Oxford OX1 3PJ ,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,29]]},"reference":[{"key":"2026092821542468400_ref1","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-025-01026-6","article-title":"Machine learning prediction of enzyme optimum pH","volume":"7","author":"Gado","year":"2025","journal-title":"Nat Mach Intel"},{"key":"2026092821542468400_ref2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbaf114","article-title":"Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature","volume":"26","author":"Qiu","year":"2025","journal-title":"Brief Bioinform"},{"key":"2026092821542468400_ref3","doi-asserted-by":"publisher","first-page":"4897","DOI":"10.1021\/acssynbio.5c00679","article-title":"Deep learning-based prediction of enzyme optimal pH and design of point mutations to improve acid resistance","volume":"14","author":"Qiu","year":"2025","journal-title":"ACS Synth Biol"},{"key":"2026092821542468400_ref4","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1007\/s00253-008-1766-x","article-title":"A novel highly acidic beta-mannanase from the acidophilic fungus Bispora sp. MEY-1: gene cloning and overexpression in Pichia pastoris","volume":"82","author":"Luo","year":"2009","journal-title":"Appl Microbiol Biotechnol"},{"key":"2026092821542468400_ref5","doi-asserted-by":"publisher","first-page":"e56146","DOI":"10.1371\/journal.pone.0056146","article-title":"Overexpression of a fungal \u03b2-mannanase from Bispora sp. MEY-1 in maize seeds and enzyme characterization","volume":"8","author":"Xu","year":"2013","journal-title":"PLoS One"},{"key":"2026092821542468400_ref6","doi-asserted-by":"publisher","first-page":"7413","DOI":"10.1038\/s41598-020-63704-2","article-title":"Author correction: characterization of novel endo-\u03b2-N-acetylglucosaminidases from Sphingobacterium species, Beauveria bassiana and cordyceps militaris that specifically hydrolyze fucose-containing oligosaccharides and human IgG","volume":"10","author":"Huang","year":"2020","journal-title":"Sci Rep"},{"key":"2026092821542468400_ref7","doi-asserted-by":"publisher","first-page":"6152","DOI":"10.1111\/j.1742-4658.2007.06136.x","article-title":"Purification and characterization of pepsins A1 and A2 from the Antarctic rock cod Trematomus bernacchii: characterizing pepsins from Antarctic fish","volume":"274","author":"Brier","year":"2007","journal-title":"FEBS J"},{"key":"2026092821542468400_ref8","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1042\/BJ20041388","article-title":"A highly acid-stable and thermostable endo-beta-glucanase from the thermoacidophilic archaeon Sulfolobus solfataricus","volume":"385","author":"Huang","year":"2005","journal-title":"Biochem J"},{"key":"2026092821542468400_ref9","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbag283","article-title":"Response to \u201caddressing flaws in the Seq2Topt dataset for the prediction of enzyme optimal temperature\u201d","volume":"27","author":"Qiu","year":"2026","journal-title":"Brief Bioinform"},{"key":"2026092821542468400_ref10","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbag002","article-title":"Machine learning for enzyme catalytic activity: current progress and future horizons","volume":"27","author":"Qiu","year":"2026","journal-title":"Brief Bioinform"},{"key":"2026092821542468400_ref11","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: the universal protein knowledgebase in 2025","volume":"53","author":"UniProt Consortium","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026092821542468400_ref12","doi-asserted-by":"publisher","first-page":"D498","DOI":"10.1093\/nar\/gkaa1025","article-title":"BRENDA, the ELIXIR core data resource in 2021: new developments and updates","volume":"49","author":"Chang","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026092821542468400_ref13","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/j.gpb.2018.11.006","article-title":"Quality matters: biocuration experts on the impact of duplication and other data quality issues in biological databases","volume":"18","author":"Chen","year":"2020","journal-title":"Genom Proteomics Bioinform"},{"key":"2026092821542468400_ref14","doi-asserted-by":"publisher","first-page":"bau016","DOI":"10.1093\/database\/bau016","article-title":"Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data","volume":"2014","author":"Poux","year":"2014","journal-title":"Database: J Biol Databases Curation"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/5\/bbag537\/71451609\/bbag537.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/5\/bbag537\/71451609\/bbag537.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T01:54:30Z","timestamp":1790646870000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag537\/8842713"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":14,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag537","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,9,1]]},"article-number":"bbag537"}}